MiniSeq / iSeq
File Structure
The file structure for a miniseq / iseq run should be correct by default, but if you are having problems uploading, please verify your file structure is correct.
.
├── CompletedJobInfo.xml
├── Alignment_1
│ └── <DateTimeFolder>
│ └── Fastq
│ ├── sample1_S1_L001_R1_001.fastq.gz
│ ├── sample1_S1_L001_R2_001.fastq.gz
│ ├── sample2_S1_L001_R1_001.fastq.gz
│ ├── sample2_S1_L001_R2_001.fastq.gz
│ ├── sample3_S1_L001_R1_001.fastq.gz
│ ├── sample3_S1_L001_R2_001.fastq.gz
│ └── <other files>
├── SampleSheet.csv
└── <other files>
Example files can be found: /examples/miniseq_run/
Preparing your miniseq / iseq sample sheet
Before using the uploader, you must prepare your sequencing run with IRIDA-specific project IDs. You must do this manually after a run completes by editing SampleSheet.csv
with Microsoft Excel or Windows Notepad.
Simply add the Sample_Project
column to the [Data]
header, and add the IRIDA project number.
An example, completed miniseq SampleSheet.csv
with the Sample_Project
column filled in looks like:
[Header]
Local Run Manager Analysis Id,3003
Date,10/27/2018
Experiment Name,20181026-MiniSeqTest
Workflow,GenerateFastQWorkflow
Description,Auto generated sample sheet. Used by workflow module to kick off Isis analysis
Chemistry,Amplicon
[Reads]
251
251
[Settings]
Adapter,ATCGATCGATCG
[Data]
Sample_ID,Sample_Name,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project
sample1-3003,sample1,ATCGAAA,N801,ATCGAAA,S801,1
sample2-3003,sample2,ATCGAAA,N801,ATCGAAA,S801,1
sample3-3003,sample3,ATCGAAA,N801,ATCGAAA,S801,1
Note: An iseq run will look almost the same, but a Description
field under [DATA]
may also be present. This is expected and the parser should function normally with the field there.